Shopify Payments is Shopify’s built-in payment processor, available on every Shopify plan in supported countries. It lets your store accept credit cards, debit cards, and digital wallets directly through Shopify without setting up a separate gateway like Stripe or PayPal. This guide covers how Shopify Payments works, which countries support it, the current fees by plan, how chargebacks are handled, how it compares to Stripe and PayPal, and when to use a third-party processor instead.

With Shopify Payments, you accept all major payment methods from the moment your store goes live. It integrates directly with Shopify checkout, order management, and financial reporting, so everything stays in one place. When you use Shopify Payments, Shopify waives its additional transaction fee, which ranges from 0.5% to 2% per sale depending on your plan.

Key Takeaways
1
Shopify Payments removes the 0.5%-2% Shopify transaction fee charged when you use a third-party gateway - on a Basic plan doing $10,000/month, that saves $200/month before processing rate differences.
2
Shopify Payments is available in 40+ countries. If your country isn’t on the list, you’ll need Stripe, PayPal, or a local gateway - but you’ll pay the Shopify transaction fee.
3
US merchants on Basic pay 2.9% + 30¢ per online transaction. The rate drops to 2.6% + 30¢ on Shopify and 2.4% + 30¢ on Advanced. Shopify Plus rates are negotiated.
4
Payouts land in your bank account in 2 business days (US), 3 business days (UK), or up to 5 business days depending on country. You can schedule payouts daily, weekly, or monthly.
5
Account holds are real. Selling restricted products, sudden chargeback spikes, or a large revenue jump can freeze payouts for days or weeks without warning. Knowing the triggers helps you avoid them.

What Countries Support Shopify Payments?

Shopify Payments is available in 40+ countries as of 2026. Below is the full list. If your country is not listed, you will need to use a third-party payment gateway such as Stripe or PayPal.

Americas

  • United States
  • Canada

Europe

  • United Kingdom
  • Ireland
  • Germany
  • France
  • Italy
  • Spain
  • Netherlands
  • Belgium
  • Sweden
  • Denmark
  • Finland
  • Norway
  • Austria
  • Switzerland
  • Czech Republic
  • Romania
  • Portugal
  • Bulgaria
  • Croatia
  • Cyprus
  • Estonia
  • Greece
  • Hungary
  • Latvia
  • Lithuania
  • Luxembourg
  • Malta
  • Poland
  • Slovakia
  • Slovenia

Asia-Pacific

  • Australia
  • New Zealand
  • Singapore
  • Hong Kong SAR
  • Japan

Most guides on this topic list only five or six countries. The full list matters because merchants in Switzerland, Singapore, or Eastern Europe often assume they cannot use Shopify Payments when they actually can. If your country appears above, you are eligible to apply during store setup or from Settings > Payments in your Shopify admin.

What Are the Charges for Shopify Payments? (2026 Pricing)

Shopify Payments fees for US merchants in 2026 (online transactions):

  • Basic Shopify: 2.9% + 30¢ per online transaction, 2.7% in person
  • Shopify: 2.6% + 30¢ online, 2.5% in person
  • Advanced Shopify: 2.4% + 30¢ online, 2.4% in person
  • Shopify Plus: Negotiated rate (typically 2.15% + 30¢ or lower depending on volume)

For merchants outside the US, rates differ by country. UK merchants on Basic pay 2% + 25p online. Canadian merchants on Basic pay 2.9% + 30¢. Australian merchants on Basic pay 1.75% + 30¢, which is lower because card network interchange fees are more competitive in Australia. European rates vary by country and plan but generally sit between 1.5% and 2.9% + a fixed fee depending on the plan tier.

There are no monthly gateway fees, setup fees, or hidden charges beyond the per-transaction rate. Shopify does not charge extra for chargebacks beyond the $15 dispute fee (covered below), and there are no additional fees for accepting Apple Pay or Google Pay.

What Are the Advantages of Using Shopify Payments?

There are several reasons Shopify merchants default to Shopify Payments over a third-party gateway.

No Shopify Transaction Fee

Shopify charges an additional transaction fee on every sale when you use a third-party gateway: 2% on Basic, 1% on Shopify, and 0.5% on Advanced. That fee disappears entirely when you use Shopify Payments. For a store doing $10,000 per month on a Basic plan, switching from Stripe to Shopify Payments saves $200 per month in transaction fees alone, before accounting for the processing rate difference.

Flexible Checkout and Payment Methods

With Shopify Payments, customers can use credit cards, debit cards, Apple Pay, Google Pay, and Shop Pay. They do not need to leave your store to complete a purchase. Shopify stores using Shopify Payments automatically meet PCI compliance requirements for secure payment processing.

You can also sell in multiple currencies and let customers see prices in their local currency at checkout. Accelerated checkout via Shop Pay means returning customers can complete a purchase in a single tap, which typically improves conversion rates on mobile.

Easy to Set Up and Use

Shopify Payments is pre-integrated with every Shopify subscription. There is no third-party account to create, no separate dashboard to log into, and no webhook configuration required. Orders and payouts both live in the same Shopify admin, which makes reconciliation straightforward.

How to Set Up Shopify Payments

Setting up Shopify Payments takes about five minutes if you have your business information ready. Here are the steps:

  1. From your Shopify admin, go to Settings and then Payments.
  2. Under “Shopify Payments,” click Complete account setup.
  3. Enter your business details: business type (individual or company), legal business name, address, and EIN or tax number depending on your country.
  4. Add your banking details so Shopify knows where to send your payouts. You will need your routing number and account number for US merchants, or the equivalent (sort code and account number in the UK, BSB in Australia).
  5. Verify your identity. Shopify uses Stripe’s identity verification on the backend, so you may be asked to upload a government-issued ID for sole proprietors or directors of companies.
  6. Review and accept the Shopify Payments terms of service.

Once approved, Shopify Payments is active immediately. Most applications are approved within minutes. In some cases, Shopify or Stripe may request additional documentation for higher-risk business categories, which can take one to two business days.

Shopify Payments vs Stripe vs PayPal: Direct Comparison

The three most common options for Shopify merchants are Shopify Payments, Stripe, and PayPal. They are not interchangeable, and the right choice depends on your country, your business type, and how much you care about the Shopify transaction fee.

PayPal is one of the three most common payment options here, and one of the most widely detected on Shopify overall. The panel below shows how widely PayPal is used across live Shopify stores.

2.4%
Share of stores in our dataset
#33
Popularity rank
11.3
Avg apps on their stores

Based on Shopify stores in our dataset · Last updated August 27, 2026.

See our PayPal usage data for the full picture.

Processing Rates

  • Shopify Payments (US Basic): 2.9% + 30¢. No Shopify transaction fee.
  • Stripe (US): 2.9% + 30¢. Plus Shopify’s 2% transaction fee on Basic = effective 4.9% + 30¢.
  • PayPal (standard checkout): 3.49% + a fixed fee. Plus Shopify’s 2% transaction fee on Basic = effective 5.49% + fee.

The numbers make Shopify Payments the clear winner on cost for most merchants. The Shopify transaction fee is what drives the math. A store doing $5,000 per month on a Basic plan pays $100 extra per month just for using Stripe instead of Shopify Payments, before comparing processing rates.

Country Availability

  • Shopify Payments: 40+ countries (listed above)
  • Stripe: 47+ countries, including India, Brazil, Mexico, and several countries where Shopify Payments is not available
  • PayPal: 200+ countries and territories - the broadest availability of any payment processor

If you are in a country where Shopify Payments is not available, Stripe is usually the next strongest option. PayPal is the fallback when neither Shopify Payments nor Stripe covers your region.

Checkout Experience

  • Shopify Payments: Fully integrated into Shopify checkout. Shop Pay accelerates repeat purchases. Customers never leave your store.
  • Stripe: Also keeps customers in your checkout, but without the Shop Pay network benefit. Setup requires a Stripe account and API key configuration.
  • PayPal: Redirects customers to the PayPal website to complete payment (in standard checkout mode), which increases drop-off. PayPal’s “Pay Later” and “Venmo” options add buyer flexibility but the redirect remains a friction point.

When to Choose Each

  • Use Shopify Payments if your country is supported, your business type is eligible, and you want the simplest setup with the lowest transaction cost.
  • Use Stripe if Shopify Payments isn’t available in your country, or if you need more developer control over the payment flow and are willing to pay the Shopify transaction fee.
  • Use PayPal as a secondary gateway alongside Shopify Payments. Many merchants run both: Shopify Payments as primary, PayPal as an alternative for customers who prefer it. This keeps your main processing costs low while capturing PayPal-preferring buyers.

How Shopify Payments Handles Chargebacks

A chargeback happens when a customer contacts their bank or card issuer to dispute a charge, rather than coming to you for a refund. When this occurs with Shopify Payments, here is what happens:

  1. Shopify notifies you by email and flags the order in your admin with a “Chargeback” label.
  2. Shopify deducts the disputed amount plus a $15 dispute fee from your next payout. This fee is charged by the card network and passed through, not charged by Shopify on top.
  3. You have a window (typically 7 to 21 days depending on the card network) to respond with evidence. Shopify gives you a form inside the admin where you can upload shipping confirmations, communication records, tracking numbers, and signed delivery receipts.
  4. If you win the dispute, the full amount including the $15 fee is refunded to you. If you lose, you keep nothing and the $15 is gone.

Shopify Payments includes basic fraud analysis tools to help you catch suspicious orders before they ship. You can also enable AVS (address verification) and CVV requirements in your payment settings to reduce fraud. For stores with higher chargeback rates, the fraud filter in Shopify Payments lets you automatically flag or hold orders that fail certain risk thresholds.

How to Get Paid Faster: Optimizing Shopify Payments Payout Timing

The standard payout schedule for Shopify Payments is 2 business days in the US after a transaction clears. That means a Monday sale arrives in your bank account on Wednesday or Thursday, depending on cut-off times. For merchants in other countries, timelines run longer: 3 business days in the UK, up to 5 business days in some European countries.

A few things affect how quickly money actually hits your account:

  • Your payout schedule setting. Shopify defaults to daily payouts, which is optimal. If you’ve changed this to weekly or monthly, change it back unless you have a specific cash-flow reason not to. Go to Settings > Payments > Payout schedule to check.
  • Your bank’s processing time. Shopify’s 2-day window is when funds leave Shopify. Your bank may take an additional 1 business day to post the deposit. Some smaller banks and credit unions process incoming ACH transfers overnight, others batch them at end of day.
  • First-time verification delay. New Shopify Payments accounts sometimes experience a 3-7 day hold on the first payout while Stripe’s identity verification system processes your information. This is a one-time thing and resolves once your account is verified.
  • Shopify Balance. If you use Shopify Balance (Shopify’s built-in business spending account), funds from sales are available instantly for use via the Shopify Balance debit card. You don’t wait for a bank transfer. For merchants who regularly reinvest revenue into ads or inventory, Shopify Balance removes the 2-day wait entirely.

There is no way to make Shopify Payments pay out faster than its standard schedule unless you use Shopify Balance. But optimizing your payout frequency to daily and keeping your bank’s ACH processing window in mind means you can often count on funds arriving within 2-3 calendar days of a sale.

Shopify Payments Account Holds: What Triggers Them and How to Avoid Them

An account hold is when Shopify or Stripe (which powers Shopify Payments) pauses your payouts while reviewing your account. Funds keep processing, but you don’t receive them until the hold is lifted. Holds can last anywhere from a few days to several weeks, and they happen without much warning.

The most common triggers for a hold:

  • Sudden revenue spike. If your store goes from $1,000 to $20,000 in sales in a week, the risk system notices the anomaly. This most often hits stores that run a viral campaign or get featured somewhere unexpectedly. The fix is to be proactive: if you’re planning a big launch, contact Shopify Payments support before it happens so they can note your account.
  • High chargeback rate. Industry average chargeback rates hover around 0.5-1%. Once your rate exceeds 1-2%, automated systems flag your account. Reducing chargebacks starts with accurate product descriptions, clear return policies, and fast order fulfillment.
  • Selling restricted or gray-area products. Supplements, CBD (even legal variants), tobacco accessories, adult content, and certain financial services all sit in categories that Stripe monitors closely. If you’re in one of these categories, review Shopify’s Terms of Service carefully before setting up Shopify Payments.
  • Refund patterns. A very high refund rate (above 10-15%) signals something is wrong to the risk system, even if the refunds are legitimate. If you’re running a business with naturally high return rates (like fashion), documenting your return policy clearly and processing refunds promptly helps avoid flags.
  • Incomplete account information. Sometimes holds happen because identity verification is incomplete or expired. Keep your business information, tax ID, and banking details current in Settings > Payments.

If your account is held, contact Shopify Support immediately via live chat or email. Have your business registration documents, recent bank statements showing legitimate business activity, and any evidence of fulfilled orders ready. Holds are often resolved within 2-5 business days once you’ve provided the requested documentation. The key is to respond quickly rather than waiting for Shopify to follow up.

Shopify Payments and Tax/Bookkeeping: What You Need to Know

Shopify Payments generates payouts, not invoices. That distinction matters for bookkeeping. Each payout you receive from Shopify Payments is a net figure - it’s your total sales minus Shopify’s processing fees for that period, minus any chargebacks or refunds. Your bank statement shows one deposit per payout cycle, not individual transaction amounts.

This creates a reconciliation challenge if you’re using accounting software. The revenue your store shows in Shopify Analytics doesn’t match the deposit in your bank account because the deposit is net of fees. To reconcile properly, you need to pull a payout report that itemizes the gross sales and the fees separately.

Where to find payout reports in Shopify:

  1. Go to Finances > Payouts in your Shopify admin.
  2. Click any individual payout to see the breakdown: gross sales, refunds, chargebacks, and fees for that pay period.
  3. You can also export a full payout report (CSV) from Analytics > Reports > Finances > Payouts.

For US merchants, Shopify issues a 1099-K if you process more than $600 in payments through Shopify Payments in a calendar year (post-2022 IRS threshold change). You’ll receive this in January for the prior tax year. The amount on the 1099-K is your gross Shopify Payments volume, not your profit. Keep your fee records to reconcile the difference when filing.

For QuickBooks and Xero integration, you’ll need a connector app - the native Shopify Payments reports don’t push directly into accounting software without one. Apps like A2X or Bold Commerce’s accounting integrations sync your Shopify Payments payouts, fee breakdowns, and refunds automatically, which saves significant reconciliation time for stores doing more than 50 orders per month.

The Cons of Shopify Payments

Shopify Payments is not the right choice for every merchant. These are the specific situations where it falls short.

Country Restriction

Shopify Payments is only available in the 40+ countries listed above. If your country is not on that list, you cannot use it at all and must rely on PayPal, Stripe (where available), or a local payment gateway supported by Shopify.

Account Holds

As covered above, Shopify - via Stripe - can place a temporary hold on your payouts if your store triggers risk flags. Merchants selling digital goods, high-ticket items, or products in gray-area categories (supplements, adult content, firearms accessories) are at higher risk of holds.

Restricted Business Categories

Shopify Payments has a list of prohibited and restricted business types. Prohibited categories include firearms, tobacco, adult content (in most cases), and certain financial services. If your store falls into a restricted category, your account may be closed without much warning. Review Shopify’s Terms of Service before applying if you are unsure whether your product type qualifies.

Limited Accounting Integration

Shopify Payments reports live inside Shopify admin. If you need clean exports to dedicated accounting software across multiple sales channels, the reconciliation requires a third-party connector app - it doesn’t work out of the box.

When NOT to Use Shopify Payments

  • You are in an unsupported country. There is no workaround. Pick Stripe, PayPal, or a local gateway instead.
  • You sell in a high-risk category. If your products are likely to trigger a Shopify Payments hold or account closure, start with a gateway that has explicit support for your category.
  • You need multi-gateway redundancy. Some high-volume merchants run two gateways simultaneously so that if one experiences downtime or a hold, the other keeps processing. Shopify Payments does not allow a second active gateway.
  • You already have excellent negotiated rates. If you process enough volume to have negotiated rates below 2.4% + 30¢ with an existing processor, switching may not save money after factoring in integration work.

Alternatives to Shopify Payments

  • PayPal: Available globally and widely trusted by buyers. Keep in mind the Shopify transaction fee still applies when using PayPal as your only gateway.
  • Stripe: Available in more countries than Shopify Payments and gives you more control over the payment flow. The Shopify transaction fee still applies when using Stripe on Shopify.
  • Other gateways: Shopify supports 100+ payment gateways worldwide. If neither Shopify Payments nor Stripe is available in your region, check the Shopify payments help page to find gateways supported for your country.

Key Information About Shopify Payments

  • No separate gateway account required; activates from your Shopify admin
  • Payout timing: 2 business days in the US, 3 business days in the UK, varies by country
  • You can set your payout schedule (daily, weekly, monthly) in Settings > Payments
  • Multi-currency supported: customers see prices in their local currency, you get paid in your store currency
  • PCI DSS compliance is handled automatically
  • Shopify Payments is not available for every business type; check the restricted categories list before applying
  • The $15 chargeback dispute fee is refunded if you win the dispute
  • For bookkeeping: each payout is net of fees - pull itemized payout reports from Finances > Payouts to reconcile